package pacBioSimple;

import java.util.List;

public class Path 
{
	private boolean begin=false;
	private boolean end=false;
	private List<StringBuilder> fullpaths = null;
	private List<StringBuilder> repeatsEndedpaths = null;
	private String toBeAlign=null;
	private List<String> stoppedTemplate = null;
	
	
	
	private StringBuilder result = null;
	
	private List<StringBuilder> fullpaths_r = null;
	private List<StringBuilder> repeatsEndedpaths_r = null;
	private String toBeAlign_r=null;
	private List<String> stoppedTemplate_R = null;
	private StringBuilder left = null;
	private StringBuilder right =null;
	
	private int begin_pos=-1;
	private int end_pos=-1;
	
	
	
	
	public int getBegin_pos() {
		return begin_pos;
	}
	public void setBegin_pos(int begin_pos) {
		this.begin_pos = begin_pos;
	}
	public int getEnd_pos() {
		return end_pos;
	}
	public void setEnd_pos(int end_pos) {
		this.end_pos = end_pos;
	}
	public boolean isBegin() {
		return begin;
	}
	public void setBegin(boolean begin) {
		this.begin = begin;
	}
	public boolean isEnd() {
		return end;
	}
	public void setEnd(boolean end) {
		this.end = end;
	}
	public StringBuilder getLeft() {
		return left;
	}
	public void setLeft(StringBuilder left) {
		this.left = left;
	}
	public StringBuilder getRight() {
		return right;
	}
	public void setRight(StringBuilder right) {
		this.right = right;
	}
	public List<StringBuilder> getFullpaths_r() {
		return fullpaths_r;
	}
	public void setFullpaths_r(List<StringBuilder> fullpaths_r) {
		this.fullpaths_r = fullpaths_r;
	}
	public List<StringBuilder> getRepeatsEndedpaths_r() {
		return repeatsEndedpaths_r;
	}
	public void setRepeatsEndedpaths_r(List<StringBuilder> repeatsEndedpaths_r) {
		this.repeatsEndedpaths_r = repeatsEndedpaths_r;
	}
	public String getToBeAlign_r() {
		return toBeAlign_r;
	}
	public void setToBeAlign_r(String toBeAlign_r) {
		this.toBeAlign_r = toBeAlign_r;
	}
	public List<String> getStoppedTemplate_R() {
		return stoppedTemplate_R;
	}
	public void setStoppedTemplate_R(List<String> stoppedTemplate_R) {
		this.stoppedTemplate_R = stoppedTemplate_R;
	}
	private boolean type =false;
	
	public List<StringBuilder> getFullpaths() {
		return fullpaths;
	}
	public void setFullpaths(List<StringBuilder> fullpaths) {
		this.fullpaths = fullpaths;
	}
	public List<StringBuilder> getRepeatsEndedpaths() {
		return repeatsEndedpaths;
	}
	public void setRepeatsEndedpaths(List<StringBuilder> repeatsEndedpaths) {
		this.repeatsEndedpaths = repeatsEndedpaths;
	}
	public String getToBeAlign() {
		return toBeAlign;
	}
	public void setToBeAlign(String toBeAlign) {
		this.toBeAlign = toBeAlign;
	}
	public List<String> getStoppedTemplate() {
		return stoppedTemplate;
	}
	public void setStoppedTemplate(List<String> stoppedTemplate) {
		this.stoppedTemplate = stoppedTemplate;
	}
	public void setType(boolean type)
	{
		this.type=type;
	}
	public boolean getType()
	{
		return this.type;
	}
	public void setResult(StringBuilder result)
	{
		this.result=result;
	}
	public StringBuilder getResult()
	{
		return this.result;
	}
	
	
	
	


	
	public String toString()
	{
		StringBuffer sb = new StringBuffer();
		if(result !=null)
		{
			sb.append("result: " +result +"\n");
		}
		else
		{
			sb.append("empty result \n");
		}
		if(this.left!=null)
		sb.append("left "+this.left+ "\n");
		else
		{
			sb.append("empty left \n");
		}
		if(this.right!=null)
		{
			sb.append("right "+this.right+"\n");
		}
		else
		{
			sb.append("empty right\n");
		}
		if(this.fullpaths!=null)
		{
			sb.append("fullpath "+this.fullpaths.toString()+"\n");
		}
		else
		{
			sb.append("empty fullpath\n");
		}
		if(this.fullpaths_r!=null)
		{
			sb.append("fullpath_r "+this.fullpaths_r.toString()+"\n");
		}
		else
		{
			sb.append("empty fullpath_r\n");
		}

		if(this.repeatsEndedpaths!=null)
		{
			sb.append("repeatsEndedpaths "+this.repeatsEndedpaths.toString()+"\n");
		}
		else
		{
			sb.append("empty repeatpath\n");
		}
		if(this.repeatsEndedpaths_r!=null)
		{
			sb.append("repeats_r "+this.repeatsEndedpaths_r.toString()+"\n");
		}
		else
		{
			sb.append("empty repeatpath_r\n");
		}
		if(this.toBeAlign!=null)
		{
			sb.append("to be align "+this.toBeAlign+"\n");	
		}
		else
		{
			sb.append("empty to be align \n" );
		}
		if(this.stoppedTemplate !=null)
		{
			sb.append("stopp Template "+this.stoppedTemplate.toString()+"\n");
		}
		else
		{
			sb.append("empty stopp template");
		}
		if(this.stoppedTemplate_R !=null)
		{
			sb.append("stopp Template_R "+this.stoppedTemplate_R.toString()+"\n");
		}
		else
		{
			sb.append("empty stopp template_R \n");
		}	
		return sb.toString();
	}
}
